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Iron in PDB 5aeu: Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400

Enzymatic activity of Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400

All present enzymatic activity of Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400:
1.14.12.18;

Protein crystallography data

The structure of Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400, PDB code: 5aeu was solved by S.Dhindwal, L.Gomez-Gil, M.Sylvestre, L.D.Eltis, J.T.Bolin, P.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.56 / 2.49
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 211.894, 211.894, 168.443, 90.00, 90.00, 120.00
R / Rfree (%) 19.3 / 25.4

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 (pdb code 5aeu). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400, PDB code: 5aeu:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 5aeu

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Iron binding site 1 out of 12 in the Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:46.3
occ:1.00
 FE1 A:FES500 0.0 46.3 1.0
ND1 A:HIS102 2.1 44.0 1.0
ND1 A:HIS123 2.1 37.0 1.0
S1 A:FES500 2.2 41.4 1.0
S2 A:FES500 2.2 42.4 1.0
FE2 A:FES500 2.9 40.9 1.0
CE1 A:HIS102 3.0 41.4 1.0
CG A:HIS123 3.1 39.2 1.0
CG A:HIS102 3.1 41.4 1.0
CE1 A:HIS123 3.1 36.5 1.0
CB A:HIS123 3.3 41.1 1.0
CB A:HIS102 3.5 40.9 1.0
N A:HIS123 3.8 41.6 1.0
CB A:TYR122 4.1 36.5 1.0
CA A:HIS123 4.1 40.8 1.0
NE2 A:HIS102 4.2 41.9 1.0
CD2 A:HIS123 4.2 37.2 1.0
N A:ARG103 4.2 40.2 1.0
NE2 A:HIS123 4.2 37.9 1.0
CD2 A:HIS102 4.2 43.8 1.0
CB A:ARG103 4.3 42.8 1.0
CG A:TYR122 4.4 32.4 1.0
SG A:CYS100 4.4 41.3 1.0
CD2 A:TYR122 4.5 33.1 1.0
SG A:CYS120 4.7 39.0 1.0
C A:TYR122 4.7 42.0 1.0
CA A:HIS102 4.7 38.8 1.0
C A:HIS102 4.7 39.4 1.0
CA A:ARG103 4.9 43.5 1.0
C A:HIS123 5.0 44.1 1.0
CA A:TYR122 5.0 38.1 1.0

Iron binding site 2 out of 12 in 5aeu

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Iron binding site 2 out of 12 in the Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:40.9
occ:1.00
 FE2 A:FES500 0.0 40.9 1.0
S1 A:FES500 2.2 41.4 1.0
S2 A:FES500 2.2 42.4 1.0
SG A:CYS120 2.3 39.0 1.0
SG A:CYS100 2.3 41.3 1.0
FE1 A:FES500 2.9 46.3 1.0
CB A:CYS100 3.0 36.7 1.0
CB A:CYS120 3.2 41.9 1.0
CB A:MET105 4.1 41.7 1.0
CB A:HIS102 4.2 40.9 1.0
CB A:TYR122 4.4 36.5 1.0
ND1 A:HIS102 4.5 44.0 1.0
CB A:TRP125 4.5 39.5 1.0
CA A:CYS100 4.5 38.0 1.0
N A:HIS123 4.6 41.6 1.0
CA A:CYS120 4.6 42.6 1.0
ND1 A:HIS123 4.7 37.0 1.0
N A:ARG103 4.7 40.2 1.0
CG A:TRP125 4.8 43.5 1.0
N A:MET105 4.8 38.2 1.0
CG A:HIS102 4.9 41.4 1.0
CG A:MET105 5.0 40.7 1.0
OH A:TYR127 5.0 42.9 1.0
N A:TYR122 5.0 37.6 1.0
C A:CYS120 5.0 42.3 1.0

Iron binding site 3 out of 12 in 5aeu

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Iron binding site 3 out of 12 in the Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:39.9
occ:1.00
 O A:HOH2059 2.0 45.5 1.0
NE2 A:HIS239 2.0 44.5 1.0
OD1 A:ASP388 2.1 33.2 1.0
O A:HOH2066 2.2 30.2 1.0
O A:HOH2063 2.2 45.4 1.0
NE2 A:HIS233 2.2 36.3 1.0
CG A:ASP388 2.8 39.6 1.0
OD2 A:ASP388 2.9 41.9 1.0
CD2 A:HIS239 3.0 41.6 1.0
CE1 A:HIS239 3.0 43.8 1.0
CE1 A:HIS233 3.1 35.0 1.0
CD2 A:HIS233 3.3 34.4 1.0
O A:HOH2105 3.4 35.5 1.0
NE2 A:GLN226 3.6 45.1 1.0
ND1 A:HIS239 4.1 43.4 1.0
CG A:HIS239 4.1 42.9 1.0
ND1 A:HIS233 4.3 37.9 1.0
CB A:ASP388 4.4 36.7 1.0
CG A:HIS233 4.4 37.6 1.0
CD A:GLN226 4.8 43.6 1.0
CB A:ALA234 4.9 39.1 1.0

Iron binding site 4 out of 12 in 5aeu

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Iron binding site 4 out of 12 in the Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe500

b:78.0
occ:1.00
 FE1 C:FES500 0.0 78.0 1.0
ND1 C:HIS123 2.2 65.0 1.0
S1 C:FES500 2.2 69.0 1.0
S2 C:FES500 2.2 62.6 1.0
ND1 C:HIS102 2.6 77.4 1.0
FE2 C:FES500 3.0 68.7 1.0
CG C:HIS123 3.1 63.7 1.0
CE1 C:HIS123 3.2 65.5 1.0
CB C:HIS123 3.3 65.8 1.0
CG C:HIS102 3.4 75.9 1.0
CE1 C:HIS102 3.5 78.9 1.0
CB C:HIS102 3.5 68.3 1.0
N C:HIS123 3.7 73.9 1.0
CB C:TYR122 3.9 59.0 1.0
CA C:HIS123 4.1 72.0 1.0
CD2 C:TYR122 4.2 54.7 1.0
CG C:TYR122 4.2 57.4 1.0
CD2 C:HIS123 4.3 61.8 1.0
NE2 C:HIS123 4.3 64.7 1.0
N C:ARG103 4.3 71.7 1.0
SG C:CYS100 4.3 71.9 1.0
CD2 C:HIS102 4.4 80.6 1.0
NE2 C:HIS102 4.5 82.4 1.0
SG C:CYS120 4.5 67.5 1.0
CB C:ARG103 4.6 76.5 1.0
C C:TYR122 4.7 68.3 1.0
CA C:HIS102 4.8 63.8 1.0
CD1 C:TRP125 4.8 69.6 1.0
NE1 C:TRP125 4.9 74.3 1.0
C C:HIS123 4.9 74.0 1.0
C C:HIS102 5.0 67.1 1.0
CA C:TYR122 5.0 62.8 1.0

Iron binding site 5 out of 12 in 5aeu

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Iron binding site 5 out of 12 in the Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe500

b:68.7
occ:1.00
 FE2 C:FES500 0.0 68.7 1.0
SG C:CYS120 2.2 67.5 1.0
S2 C:FES500 2.2 62.6 1.0
S1 C:FES500 2.2 69.0 1.0
SG C:CYS100 2.3 71.9 1.0
FE1 C:FES500 3.0 78.0 1.0
CB C:CYS100 3.1 64.5 1.0
CB C:CYS120 3.2 65.9 1.0
CB C:MET105 4.1 61.1 1.0
CB C:TYR122 4.2 59.0 1.0
CB C:HIS102 4.5 68.3 1.0
N C:HIS123 4.6 73.9 1.0
CA C:CYS100 4.6 66.0 1.0
CA C:CYS120 4.6 66.2 1.0
CB C:TRP125 4.7 67.0 1.0
N C:MET105 4.8 62.6 1.0
CG C:TRP125 4.9 69.5 1.0
ND1 C:HIS123 4.9 65.0 1.0
N C:ARG103 5.0 71.7 1.0
CA C:MET105 5.0 65.4 1.0

Iron binding site 6 out of 12 in 5aeu

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Iron binding site 6 out of 12 in the Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:43.1
occ:1.00
 O C:HOH2025 1.8 28.8 1.0
O C:HOH2022 1.9 47.9 1.0
OD1 C:ASP388 2.0 42.6 1.0
NE2 C:HIS239 2.0 46.0 1.0
NE2 C:HIS233 2.0 46.3 1.0
O C:HOH2020 2.4 40.7 1.0
CE1 C:HIS233 3.0 49.6 1.0
CG C:ASP388 3.0 40.7 1.0
CD2 C:HIS239 3.0 45.2 1.0
CE1 C:HIS239 3.0 47.0 1.0
CD2 C:HIS233 3.1 49.2 1.0
OD2 C:ASP388 3.3 43.7 1.0
O C:HOH2043 3.4 47.3 1.0
NE2 C:GLN226 3.5 46.3 1.0
ND1 C:HIS233 4.1 49.1 1.0
ND1 C:HIS239 4.1 45.6 1.0
CG C:HIS239 4.1 43.5 1.0
CG C:HIS233 4.2 45.5 1.0
CB C:ASP388 4.4 39.5 1.0
CD C:GLN226 4.7 47.4 1.0
CA C:ASP388 5.0 40.4 1.0

Iron binding site 7 out of 12 in 5aeu

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Iron binding site 7 out of 12 in the Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe500

b:47.7
occ:1.00
 FE1 E:FES500 0.0 47.7 1.0
ND1 E:HIS123 2.2 41.7 1.0
S1 E:FES500 2.2 45.4 1.0
S2 E:FES500 2.2 42.0 1.0
ND1 E:HIS102 2.3 53.3 1.0
FE2 E:FES500 2.8 46.8 1.0
CG E:HIS123 3.1 40.6 1.0
CG E:HIS102 3.2 52.3 1.0
CE1 E:HIS123 3.2 41.9 1.0
CE1 E:HIS102 3.3 51.5 1.0
CB E:HIS123 3.3 44.9 1.0
CB E:HIS102 3.4 51.5 1.0
N E:HIS123 3.9 44.4 1.0
CB E:TYR122 4.1 41.1 1.0
CA E:HIS123 4.1 48.2 1.0
CD2 E:HIS123 4.2 43.1 1.0
NE2 E:HIS123 4.3 44.5 1.0
N E:ARG103 4.3 53.2 1.0
CG E:TYR122 4.3 42.7 1.0
CD2 E:HIS102 4.3 53.2 1.0
NE2 E:HIS102 4.3 54.5 1.0
CD2 E:TYR122 4.4 41.5 1.0
CB E:ARG103 4.4 49.5 1.0
SG E:CYS120 4.6 49.9 1.0
C E:TYR122 4.6 45.0 1.0
CA E:HIS102 4.7 50.5 1.0
SG E:CYS100 4.7 49.2 1.0
C E:HIS102 4.8 51.5 1.0
CA E:ARG103 4.9 48.8 1.0
CD1 E:TRP125 5.0 53.1 1.0
CA E:TYR122 5.0 45.1 1.0
C E:HIS123 5.0 50.8 1.0

Iron binding site 8 out of 12 in 5aeu

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Iron binding site 8 out of 12 in the Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe500

b:46.8
occ:1.00
 FE2 E:FES500 0.0 46.8 1.0
S1 E:FES500 2.2 45.4 1.0
S2 E:FES500 2.2 42.0 1.0
SG E:CYS120 2.4 49.9 1.0
SG E:CYS100 2.4 49.2 1.0
FE1 E:FES500 2.8 47.7 1.0
CB E:CYS100 3.1 48.9 1.0
CB E:CYS120 3.3 50.7 1.0
CB E:HIS102 4.1 51.5 1.0
CB E:TYR122 4.4 41.1 1.0
CB E:TRP125 4.4 54.0 1.0
CB E:MET105 4.5 45.6 1.0
CA E:CYS100 4.5 52.3 1.0
N E:HIS123 4.6 44.4 1.0
CG E:TRP125 4.6 56.0 1.0
ND1 E:HIS102 4.6 53.3 1.0
N E:ARG103 4.7 53.2 1.0
CA E:CYS120 4.7 51.1 1.0
ND1 E:HIS123 4.8 41.7 1.0
CG E:HIS102 4.8 52.3 1.0
N E:MET105 4.9 47.2 1.0
C E:CYS100 4.9 53.7 1.0
CD2 E:TRP125 4.9 57.7 1.0
N E:HIS102 5.0 52.2 1.0
OH E:TYR127 5.0 50.3 1.0
CA E:HIS102 5.0 50.5 1.0

Iron binding site 9 out of 12 in 5aeu

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Iron binding site 9 out of 12 in the Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:71.2
occ:1.00
 NE2 E:HIS239 2.1 65.5 1.0
NE2 E:HIS233 2.2 67.5 1.0
OD1 E:ASP388 2.3 64.5 1.0
O E:HOH2013 2.4 56.4 1.0
O E:HOH2012 2.6 41.4 1.0
O E:HOH2017 2.7 52.2 1.0
OD2 E:ASP388 2.7 64.2 1.0
CG E:ASP388 2.9 63.7 1.0
CE1 E:HIS233 2.9 72.6 1.0
CE1 E:HIS239 3.1 67.2 1.0
CD2 E:HIS239 3.1 68.5 1.0
CD2 E:HIS233 3.4 67.4 1.0
NE2 E:GLN226 3.6 57.9 1.0
ND1 E:HIS233 4.2 72.2 1.0
ND1 E:HIS239 4.2 67.9 1.0
CG E:HIS239 4.3 69.3 1.0
CB E:ASP388 4.4 58.4 1.0
CG E:HIS233 4.4 69.7 1.0
CD E:GLN226 4.7 58.8 1.0

Iron binding site 10 out of 12 in 5aeu

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Iron binding site 10 out of 12 in the Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of II9 Variant of Biphenyl Dioxygenase From Burkholderia Xenovorans LB400 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe500

b:78.4
occ:1.00
 FE1 G:FES500 0.0 78.4 1.0
CD2 G:HIS123 2.1 65.1 1.0
ND1 G:HIS102 2.1 59.8 1.0
S1 G:FES500 2.2 70.8 1.0
S2 G:FES500 2.2 73.6 1.0
CG G:HIS123 2.8 68.7 1.0
CE1 G:HIS102 2.9 57.9 1.0
FE2 G:FES500 3.1 75.2 1.0
CB G:HIS123 3.1 70.9 1.0
CG G:HIS102 3.2 59.7 1.0
NE2 G:HIS123 3.2 68.9 1.0
CB G:HIS102 3.6 61.0 1.0
N G:HIS123 3.8 68.6 1.0
CB G:TYR122 4.0 58.6 1.0
ND1 G:HIS123 4.0 72.2 1.0
NE2 G:HIS102 4.1 59.4 1.0
CA G:HIS123 4.1 72.6 1.0
CG G:TYR122 4.2 56.2 1.0
CD2 G:HIS102 4.2 59.7 1.0
CE1 G:HIS123 4.2 72.2 1.0
CD2 G:TYR122 4.3 57.7 1.0
CB G:ARG103 4.3 65.2 1.0
C G:TYR122 4.5 68.1 1.0
N G:ARG103 4.5 71.0 1.0
SG G:CYS120 4.6 69.6 1.0
SG G:CYS100 4.6 67.4 1.0
CA G:TYR122 4.8 65.2 1.0
CA G:HIS102 4.9 65.0 1.0
C G:HIS102 5.0 68.3 1.0
CD1 G:TYR122 5.0 56.9 1.0

Reference:

P.Kumar, S.Dhindwal, D.Neau, L.Gomez-Gil, M.Sylvestre, L.D.Eltis, J.T.Bolin. Structural Basis of the Enhanced Pollutant-Degrading Capabilities of An Engineered Biphenyl Dioxygenase J.Bacteriol. V. 198 1499 2016.
ISSN: ISSN 0021-9193
PubMed: 26953337
DOI: 10.1128/JB.00952-15
Page generated: Mon Aug 5 19:35:16 2024

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